ITGB5

integrin subunit beta 5, the group of Integrin beta subunits

Basic information

Region (hg38): 3:124761948-124901418

Links

ENSG00000082781 ∙ NCBI:3693 ∙ OMIM:147561 ∙ HGNC:6160 ∙ Uniprot:P18084 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ITGB5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGB5 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			46	1		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	1	1

Variants in ITGB5

This is a list of pathogenic ClinVar variants found in the ITGB5 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-124763666-G-A		not specified	Uncertain significance (Nov 19, 2022)
3-124764402-G-A		not specified	Uncertain significance (May 27, 2022)
3-124764405-C-T		not specified	Uncertain significance (Jan 30, 2024)
3-124764417-C-T		not specified	Uncertain significance (Dec 16, 2023)
3-124764418-G-T		not specified	Uncertain significance (Aug 23, 2021)
3-124764537-C-T		not specified	Uncertain significance (Dec 19, 2022)
3-124764545-G-C		not specified	Uncertain significance (Sep 25, 2023)
3-124769077-T-A		not specified	Uncertain significance (Feb 27, 2023)
3-124773882-T-C		not specified	Uncertain significance (Aug 02, 2021)
3-124773892-C-T		not specified	Uncertain significance (Nov 15, 2023)
3-124796426-T-C		not specified	Uncertain significance (Sep 29, 2023)
3-124796507-C-T		not specified	Uncertain significance (Feb 03, 2022)
3-124796513-C-T		not specified	Uncertain significance (Dec 21, 2022)
3-124796541-G-A		not specified	Uncertain significance (Oct 27, 2023)
3-124796573-C-G		not specified	Uncertain significance (Apr 18, 2024)
3-124796586-C-T		not specified	Uncertain significance (Nov 10, 2022)
3-124796733-G-A		not specified	Uncertain significance (Aug 12, 2021)
3-124796742-C-T		not specified	Uncertain significance (May 25, 2022)
3-124796776-G-C		not specified	Uncertain significance (Jul 06, 2021)
3-124796798-A-G		not specified	Uncertain significance (Nov 13, 2023)
3-124809032-A-G		not specified	Uncertain significance (Jul 06, 2021)
3-124809149-C-T		not specified	Uncertain significance (Oct 10, 2023)
3-124817650-T-C		not specified	Uncertain significance (Oct 10, 2023)
3-124817664-C-T		not specified	Uncertain significance (Jun 06, 2023)
3-124819774-A-C		not specified	Uncertain significance (Mar 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITGB5	protein_coding	protein_coding	ENST00000296181	15	139471

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.89e-8	0.999	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	406	471	0.862	0.0000277	5262
Missense in Polyphen		187	230.51	0.81124		2473
Synonymous	0.332	190	196	0.970	0.0000124	1544
Loss of Function	2.98	18	37.8	0.476	0.00000195	440

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000203	0.000202
Middle Eastern	0.00	0.00
South Asian	0.000197	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Integrin alpha-V/beta-5 (ITGAV:ITGB5) is a receptor for fibronectin. It recognizes the sequence R-G-D in its ligand.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);ECM-receptor interaction - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Dilated cardiomyopathy (DCM) - Homo sapiens (human);Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human);Phagosome - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);VEGF Signaling Pathway;Integrin-mediated Cell Adhesion;Arrhythmogenic Right Ventricular Cardiomyopathy;miRNA targets in ECM and membrane receptors;Focal Adhesion;VEGFA-VEGFR2 Signaling Pathway;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Smooth Muscle Contraction;Integrin cell surface interactions;Extracellular matrix organization;Immune System;Adaptive Immune System;Molecules associated with elastic fibres;Elastic fibre formation;Antigen processing-Cross presentation;Class I MHC mediated antigen processing & presentation;Muscle contraction;Integrin;Cross-presentation of particulate exogenous antigens (phagosomes);Syndecan interactions;Non-integrin membrane-ECM interactions;Leptin;ECM proteoglycans;Beta5 beta6 beta7 and beta8 integrin cell surface interactions;Signaling events mediated by focal adhesion kinase;Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling;Regulation of nuclear SMAD2/3 signaling (Consensus)

Recessive Scores

• pRec: 0.221

Intolerance Scores

• loftool: 0.0949
• rvis_EVS: -0.28
• rvis_percentile_EVS: 33.53

Haploinsufficiency Scores

• pHI: 0.509
• hipred: Y
• hipred_score: 0.706
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.833

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Itgb5
• Phenotype: neoplasm; normal phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); immune system phenotype; vision/eye phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype

Gene ontology

• Biological process: antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent;muscle contraction;cell-matrix adhesion;transforming growth factor beta receptor signaling pathway;integrin-mediated signaling pathway;cell migration;extracellular matrix organization;cell adhesion mediated by integrin;endodermal cell differentiation;stress fiber assembly;viral entry into host cell;epithelial cell-cell adhesion
• Cellular component: plasma membrane;focal adhesion;integrin complex;cell surface;integrin alphav-beta5 complex;receptor complex;phagocytic vesicle;extracellular exosome
• Molecular function: virus receptor activity;integrin binding;protein binding;signaling receptor activity